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Hyperlink to GenomeBrowse from another application?

asked 2015-07-20 03:01:26 -0600

Siavosh Taba gravatar image


I have tried to find an answer for the above question. Right now I have an Excel-file with an long number of positions I want to check, and I have to Copy/Paste Chr:Position into GenomeBrowse every time.

This is quite ineffective, so I thought that there maybe was a way to launch GenomBrowse using a hyperlink. However, there doesn't seem to be any documentation for it.

Are there any launch parameters/arguments for GenomeBrowse? So I could write something in excel like:

=HYPERLINK("C:\Path_to_folder\GenomeBrowse.exe -position", Chromosome:Position)

If not, it would be an appreciated function for the next version of GenomeBrowse :)

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answered 2015-07-20 11:45:13 -0600

HI Siavosh,

I am happy to help with your hyperlink questions.

You can link to GenomeBrowse from third party software (ex. Excel, Evernote...) by using a simple html hyperlink similar to the URL: genomebrowse:/api/zoom?locus=chr1:476471220-47647338.

Excel does not really like this URL format inside their HYPERLINK function so in the below example I used the CONCATENATE function to create the full strings before forming the hyperlinks.

image description

So starting from a spreadsheet with at least chromosome, start and stop position you automatically create the hyperlinks by adding following additional columns.

image description

If you click the links GenomeBrowse should open and zoom to that location or just perform the zoom if GenomeBrowse is already running.

Let me know if you have any issues or further questions.

Thanks, Jami...

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Thanks for the help :) It works like a charm.

Siavosh Taba ( 2015-07-22 01:27:09 -0600 )edit
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Asked: 2015-07-20 03:01:26 -0600

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Last updated: Jul 20 '15